Chemical pesticides can present toxic effects to human beings, and they are classified based on chemical characterization, presenting 300 active substances and more than 2000 different formulations. Their overuse can represent a significant risk factor to human health. Therefore, it is essential to investigate the putative association between health harms and pesticides because this information can be helpful for monitoring and controlling pesticide exposure. This study aims to analyze secondary data about pesticides and their effects on genes and disease phenotypes leading to health harm. For this, we used information about pesticides available on the Ministry of Agriculture, Livestock Breeding, and Supply documents. We also use the Set Analyzer tool available on the Comparative Toxicogenomics Database (CTD) to verify a putative association between pesticides and their specific chemical groups to human diseases. Finally, we use variance analysis to evaluate them for statistical purposes. Results showed that 127 chemical groups could be found in food, and they are classified into eight functional classes of pesticides used against pests in food crops. These functional classes are acaricides, bactericides, fungicides, herbicides, insecticides, molluscicides, nematicides, and plant growth regulators. Furthermore, data obtained from the CTD showed a predominance of digestive, nervous, respiratory, and skin diseases as the significant harms caused by pesticide exposure. Results also showed that all the pesticides’ functional classes affect genes associated with cancer development. Considering all the 127 chemical groups, we identified 145321 genes affected by these substances: 49733 genes affected by acaricides, 26832 genes affected by fungicides, 22687 genes affected by herbicides, 42681 genes affected by insecticides, 15842 genes affected by molluscicides, 15842 genes affected by nematicides, and 17217 genes affected by plant growth regulators. Organophosphates are the primary chemical group responsible for genetic effects, mainly leading to cancer and nervous system diseases. So, we conclude that seven different chemical groups can affect genes associated with cancer development and also concluded pesticide use could be related to genes effects and diseases development which can lead to health harms.